How can I composite these 3 Layers?
You can't compose this way because you use Glass shadier on the window. Glass isn't just transparent color - it have refraction and reflection, that's why it renders non-transparent. So you can try different things:

1. Just remove window or move it on different layer.

Then use Mask layer. If I move window on this layer:

 

The setup for render layer flames will look like (pay attention to the mask layer option):



and door of course:



result will be look like:



2. add glow effect by threshold 

in this case you should not to separate render layers. Render all in one frame and in glare node set threshold to value between 0 and 1